The Sand Gnats won for the ninth time in 10 games since the All-Star break, peppering Augusta starter Mike Kickham for eight runs on 12 hits before he was pulled with two outs in the sixth.
The GreenJackets twice loaded the bases with one out and failed to score either time. They stranded 10 runners to raise their league-leading total to 605 for the season, an average of more than 7.5 per game.
"We left a lot of guys on base again. We've got to improve the approach we make at the plate," manager Lipso Nava said. "Once that guy gets to second base, we change our mentality. We need to have a better idea of what we're doing at the plate in that situation."
Six of the 10 base runners had advanced to at least second base before being stranded on a night when Augusta went 1 for 10 with runners in scoring position.
The lost runs proved costly against a team that has played near perfect ball since the second half started. The Sand Gnats won their eighth consecutive game and 11th in 13 meetings with Augusta this year.
"We've got a few one-run games on them, so it's not like we're absolutely blowing them out every night," Savannah manager Ryan Ellis said. "On any given night it's just been one hit better."
Savannah starter Gonzalez Germen (6-3) got the win after scattering six hits in five shutout innings.
He gave up three consecutive singles in the first inning but got out of the jam with Devin Harris' first of three strikeouts and a Ryan Scoma grounder to first.
"That was huge," Ellis said. "We get away with that with no runs, and Germen just seemed to get better after that as the game went on."
Another prime scoring opportunity with the bases loaded was squandered by Augusta when Bobby Haney grounded into a double play to end the fifth.
Aderlin Rodriguez went 3 for 4 with two RBI and was one of four Sand Gnats to post multiple hits. His ground-rule double was one of five Sand Gnats hits in their five-run third.
Kickham (1-5) dropped his fourth consecutive decision. He gave way to Mario Rodriguez, who needed only two pitches to end the sixth before Seth Rosin allowed one hit over three shutout innings.
The GreenJackets (3-7, 34-47) will try to avoid a sweep when the three-game series wraps up tonight with a special Sunday start time of 7:05 p.m.